A di­deoxy­dide­hydro­nucleoside derivative

We have synthesized a di­deoxy­dide­hydro­nucleoside derivative, 2(S)‐acetoxymethyl‐4‐[4‐amino‐2‐oxopyrimidin‐1(2H)‐yl]‐2,5‐di­hydro­furan, C₁₁H₁₃N₃O₄, which is an analogue of the potently anti‐HIV active compound, di­deoxy‐dide­hydro­cytidine (d4C). The target compound crystallizes with two mol­ecules in the asymmetric unit that differ primarily in the orientation of the C6′‐acetyl group. One mol­ecule has an extended conformation and the orientation of the acetyl group in the second mol­ecule gives an unusual hooked‐shaped conformation. The two conformers form A–B dimers via N—H?N hydrogen bonds. The dimers link via N—H?O hydrogen bonds to form chains parallel to the b cell axis.     

Two carbamoyl‐substituted di­hydro­pyrimidines: potential mimics of di­hydro­pyridine calcium channel blockers

The structures of two conformationally similar 1,4‐di­hydro­pyrimidines with a novel carbamoyl substitution, viz. 6‐methyl‐5‐(N‐methyl­carbamoyl)‐4‐phenyl‐1,2,3,4‐tetrahydro­py­rimidine‐2‐thione monohydrate, C₁₃H₁₅N₃OS·H₂O, (I), and 4‐(4‐chloro­phenyl)‐6‐methyl‐5‐(N‐methyl­carbamoyl)‐1,2,3,4‐tetra­hydro­pyrimidine‐2‐thione monohydrate, C₁₃H₁₄ClN₃OS·H₂O, (II), exhibit the structural features of 1,4‐di­hydro­pyridine calcium channel blockers. In both structures, the pyrimidine ring adopts a flattened boat conformation and the carbamoyl side chain is in an extended conformation with an anticlinal orientation. The phenyl ring occupies a pseudo‐axial position with respect to the pyrimidine ring in these structures. Both compounds crystallize with one mol­ecule of water, which participates in a two‐dimensional hydrogen‐bonding network. The mol­ecules are linked into dimers by N—H·S hydrogen bonds in both structures.     

A non‐natural dinucleotide containing an isomeric l‐related deoxy­nucleoside: dinucleotide inhibitors of anti‐HIV integrase activity

The first X‐ray crystal structure of a non‐natural dinucleotide, 5′‐O‐phosphoryl‐1′‐deoxy‐2′‐isoadenylyl‐(3′ → 5′)‐cytidine 6.5‐hydrate (pIsodApC), C₁₉H₂₆N₈O₁₃P₂·6.5H₂O, belonging to a family of dinucleotides that contain an isomeric nucleoside component, is described. A complex system of hydrogen bonds between water mol­ecules and various sites on the dinucleotide was found. All H atoms were located from electron‐density difference maps, which allowed identification of protonation sites. Compounds of this family have been found to bind at the active site of HIV integrase and to be inhibitors of this key viral enzyme. These dinucleotides are completely resistant to cleavage by exonucleases; an abnormal dihedral angle twist in an inter­nucleotide phosphate bond revealed in the X‐ray crystal structure may be contributing to this unusual stability towards nucleases.     

Two isomeric cucurbitane derivatives

Two isomeric cucurbitane derivatives, 3β,7α,11β‐triacetoxycucurbit‐5(10)‐ene, (I), and 3β,7α,11β‐triacetoxy‐5α‐cucurbit‐1(10)‐ene, (II), both C₃₆H₅₈O₆, have their single endocyclic C=C double bonds in different positions. This results in differences in the conformation of the four‐ring system, which is close to a half‐chair/half‐chair/chair/half‐chair arrangement in (I) and to a half‐chair/twist‐boat/boat/half‐chair arrangement in (II). The orientation of some of the substituents is also different; the 3β‐acetoxy group is in an equatorial position in (I) but in an axial position in (II), while the 11β‐acetoxy group occupies an axial position in (I) and an equatorial position in (II). The asymmetric unit of (I) contains two symmetry‐independent molecules which do not differ significantly, being related by a pseudo‐twofold axis of symmetry. In both structures, the aliphatic chain fragments are disordered and the disorder persists at lower temperatures.     

Two polymorphs of bis(2‐bromophenyl) di­sulfide

Colourless crystals of the title compound, bis(2‐bromo­phenyl) di­sulfide, C₁₂H₈Br₂S₂, are obtained from the reaction of 2‐bromo­phenyl­mercaptan with metallic sodium and either zinc chloride or cadmium chloride in methanol. In the presence of Zn^II ions, the crystals are orthorhombic (space group Pbca, with Z′ = 1); with Cd^II ions present, the product is triclinic (space group , with Z′ = 4). Both polymorphs exhibit significant intramolecular C—H⋯S hydrogen bonds. In the ortho­rhombic form, mol­ecules are linked by intermolecular C—H⋯Br hydrogen bonds, while in the triclinic form, mol­ecules exhibit Br⋯Br contacts.     

Zirconium di­hydroxide chromate

The crystal structure of the title compound, Zr(OH)₂CrO₄, has been reinvestigated [Mark (1972). Acta Chem. Scand. 26 , 3744–3756]. It is composed of ordered layers whose stacking in the c direction is disordered. The symmetry of the superposition structure is tetragonal, space group I4₁/amd with a = 6.8709 (1) and c = 29.0432 (2) Å. The true 0D structure has ordered layers of the dimensions a_L = b_L = 2a and c₀ = c/4, where c₀ is the spacing between adjacent layers. The Zr atoms are joined by double hydroxide bridges and the structure consists of infinite nets with the composition [Zr₃(OH)₆CrO₄]_n⁴ⁿ⁺, joined together in c direction by chromate groups. The zirconium polyhedra are not influenced by the 0D phenomenon.     

Pyridinium di­hydrogenmono­thio­phosphate

By reaction of pyridine di­thio­monometa­phospho­ryl fluoride with ethyl­di­phenyl­phosphine in the presence of traces of water, we isolated crystals of the title compound, (I). In the structure of this salt, two kinds of hydrogen bonds were detected. They link N—H (part of the cation), as well as one O—H group (part of the anion), to the phospho­ryl O atom of the anion. The donor–acceptor distances are 2.654 (1) and 2.568 (1) Å, respectively. The P—O and P—S bond lengths are 1.514 (2) and 1.967 (1) Å, respectively, which fall therefore in the range of a 1.5‐fold bond.     

Two new polymorphs of di­phenyl(4‐pyridyl)­methyl methacryl­ate

The title compound (D4PyMA), C₂₂H₁₉NO₂, exhibits polymorphism after crystallization by slow evaporation from a binary mixture of chloro­form and hexane. Long needle‐like crystals have an orthorhombic structure (space group Fdd2), with one mol­ecule in the asymmetric unit, while small tablet‐like crystals exhibit a monoclinic crystal structure (space group P2₁/n), in which two independent but chemically identical mol­ecules comprise the asymmetric unit. The bond lengths and angles are normal, while the torsion angles around the –C—O– bond linking the di­phenyl(4‐pyridyl)methyl and methacryl­ate groups show the flexibility of the mol­ecule by way of packing effects. The two polymorphs both contain weak C—H⋯π and C—H⋯O/N contacts but have different conformations.     

1‐Chloro‐3,6‐di­methoxy‐2,5‐di­methyl­benzene and 1‐chloro‐3,6‐di­methoxy‐2,4‐di­methyl­benzene

The title compounds, 1‐chloro‐3,6‐di­methoxy‐2,5‐di­methyl­benzene, (IIIa), and 1‐­chloro‐3,6‐di­methoxy‐2,4‐di­methyl­benzene, (IIIb), both C₁₀H₁₃ClO₂, were obtained from 2,5‐ and 2,6‐di­methyl‐1,4‐benzo­quinone, respectively, and are intermediates in the synthesis of ammonium quinone derivatives. The isomers have different substituents around the methoxy groups and crystallize in different space groups. In both mol­ecules, the methoxy groups each have different orientations with respect to the benzene ring. In both cases, one methoxy group lies in the plane of the ring and can participate in conjugation with the aromatic system, while the second is almost perpendicular to the plane of the aromatic ring. The C—O—C bond angles around these substituents are also different: 117.5 (4) and 118.2 (3)° in (IIIa) and (IIIb), respectively, when the methoxy groups lie in the plane of the ring, and 114.7 (3) and 113.6 (3)° in (IIIa) and (IIIb), respectively, when they are out of the plane of the ring.     

Di­propyl 3,6‐di­phenyl‐1,2‐di­hydro‐1,2,4,5‐tetrazine‐1,2‐di­carboxyl­ate

The title compound, C₂₂H₂₄N₄O₄, was prepared from propyl chloro­formate and 3,6‐di­phenyl‐1,2‐di­hydro‐s‐tetrazine. This reaction yields the title compound rather than di­propyl 3,6‐di­phenyl‐1,4‐di­hydro‐s‐tetrazine‐1,4‐di­carboxyl­ate. The 2,3‐di­aza­buta­diene group in the central six‐membered ring is not planar; the C=N double‐bond length is 1.285 (2) Å, and the average N—N single‐bond length is 1.401 (3) Å, indicating a lack of conjugation. The ring has a twist conformation, in which adjacent N atoms lie 0.3268 (17) Å from the plane of the ring. The mol­ecule has twofold crystallographic symmetry.     

6‐Aza‐2′‐deoxy­uridine and N3‐anisoyl‐6‐aza‐2′‐deoxy­uridine

In 2‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐1,2,4‐triazine‐3,5(2H,4H)‐dione (6‐aza‐2′‐deoxy­uridine), C₈H₁₁N₃O₅, (I), the conformation of the glycosylic bond is between anti and high‐anti [χ = −94.0 (3)°], whereas the derivative 2‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐N⁴‐(2‐methoxy­benzoyl)‐1,2,4‐triazine‐3,5(2H,4H)‐dione (N³‐anisoyl‐6‐aza‐2′‐deoxy­uridine), C₁₆H₁₇N₃O₇, (II), displays a high‐anti conformation [χ = −86.4 (3)°]. The furanosyl moiety in (I) adopts the S‐type sugar pucker (²T₃), with P = 188.1 (2)° and τ_m = 40.3 (2)°, while the sugar pucker in (II) is N (³T₄), with P = 36.1 (3)° and τ_m = 33.5 (2)°. The crystal structures of (I) and (II) are stabilized by inter­molecular N—H⋯O and O—H⋯O inter­actions.     

Calculations of 1H NMR coupling constants for conformational studies of isomeric pentofuranosyl nucleosides

The SCF FPT method in the INDO approximation of molecular orbital theory is employed for calculations of ¹H NMR cisoidal coupling constants in model compounds. Obtained results are used for finding conformational states of α-xylo-, β-lyxo-, and α-2′-deoxyribonucleosides in solution.     

Bis­[2‐(di­phenyl­phosphinoyl)­benzene] di­sulfide

The title compound, [2‐Ph₂P(O)C₆H₄S]₂ or C₃₆H₂₈O₂P₂S₂, obtained by electrochemical oxidation of 2‐(di­phenyl­phosphino)­benzene­thiol, has twofold crystallographic symmetry. Principal dimensions include S—S 2.0212 (15) Å, S—C 1.786 (3) Å and C—S—S—C 81.34 (14)°.     

7‐Deaza‐2′‐deoxy­guanosine

In the title compound, 2‐amino‐7‐(2‐deoxy‐β‐d ‐erythro‐pentofuran­osyl)‐3,7‐dihydro­pyrrolo[2,3‐d]pyrimidin‐4‐one, C₁₁H₁₄N₄O₄, the N‐glycosylic bond torsion angle, χ, is anti [−106.5 (3)°]. The 2′‐deoxy­ribofuran­osyl moiety adopts the ³T₄ (N‐type) conformation, with P = 39.1° and τ_m = 40.3°. The conformation around the exocyclic C—C bond is ap (trans), with a torsion angle, γ, of −173.8 (3)°. The nucleoside forms a hydrogen‐bonded network, leading to a close‐packed multiple‐layer structure with a head‐to‐head arrangement of the bases. The nucleobase interplanar O=C—C⋯NH₂ distance is 3.441 (1) Å.     

Bis(μ‐hexa­methyl­enetetr­amine)­bis(aqua­di­bromo­cadmium)­di­aqua­di­bromo­cadmium dihydrate

The title compound, poly­[[di­aqua­di­bromo­cadmium‐μ‐(1,3,5,7‐tetra­aza­tri­cyclo[3.3.1.1^3,7]decane‐N¹:N⁵)‐aqua­cad­mium‐di‐μ‐bromo‐aqua­cadmium‐μ‐(1,3,5,7‐tetra­aza­tri­cyclo[3.3.1.1^3,7]decane‐N¹:N⁵)‐di‐μ‐bromo] dihydrate], [Cd₃­Br₆­(C₆­H₁₂­N₄)₂­(H₂O)₄]·­2H₂O, is made up of two‐dimensional neutral rectangular coordination layers. Each rectangular subunit is enclosed by a pair of Cd₃(μ₂‐Br)₆(H₂O)₃ fragments and a pair of (μ₂‐hmt)Cd(H₂O)₂Br₂(μ₂‐hmt) fragments as sides (hmt is hexa­methyl­enetetr­amine). The unique Cd^II atom in the Cd₂Br₂ ring in the Cd₃(μ₂‐Br)₆(H₂O)₃ fragment is in a slightly distorted octahedral CdNOBr₄ geometry, surrounded by one hmt ligand [2.433 (5) Å], one aqua ligand [2.273 (4) Å] and four Br atoms [2.6409 (11)–3.0270 (14) Å]. The Cd^II atom in the (μ₂‐hmt)Cd(H₂O)₂Br₂(μ₂‐hmt) fragment lies on an inversion center and is in a highly distorted octahedral CdN₂O₂Br₂ geometry, surrounded by two trans‐related N atoms of two hmt ligands [2.479 (5) Å], two trans‐related aqua ligands [2.294 (4) Å] and two trans‐related Br atoms [2.6755 (12) Å]. Adjacent two‐dimensional coordination sheets are connected into a three‐dimensional network by hydrogen bonds involving lattice water mol­ecules, and the aqua, bromo and hmt ligands belonging to different layers.     

Conformation of cationic N,N‐di­methyl­glycine in di­methyl­glycinium tri­fluoro­acetate

In the title compound, C₄H₁₀NO₂⁺·C₂F₃O₂^?, the main N—C—COOH skeleton of the protonated amino acid is nearly planar. The C=O/C—N and C=O/O—H bonds are syn and the two methyl groups are gauche to the methyl­ene H atoms. The conformation of the cation in the crystal is compared to that given by ab initio calculations (Hartree–Fock, self‐consistent field molecular‐orbital theory). The tri­fluoro­acetate anion has the typical staggered conformation with usual bond distances and angles. The cation and anion form dimers through a strong O—H?O hydrogen bond which are further interconnected in infinite zigzag chains running parallel to the a axis by N—H?O bonds. Weaker C—H?O interactions involving the methyl groups and the carboxy O atoms of the cation occur between the chains.     

Diethyl 4‐(2,5‐di­methoxy­phenyl)‐2,6‐di­methyl‐1,4‐di­hydro­pyridine‐3,5‐di­carboxyl­ate,conformational change with solvent of crystallization

The title compound, C₂₁H₂₇NO₆, has been crystallized from ethanol containing nitro­benzene and shows the phenyl ring, B, in an ap conformation. This structure may be compared with that of the mol­ecule crystallized from ethanol alone, in which the B ring is seen in an sp conformation. The isolation of this rotamer has implications for the understanding of the docking of calcium beta‐blocking di­hydro­pyridine mol­ecules with their receptor site.     

Diethyl 3,8‐di­methyl‐4,7‐di­aza­deca‐2,8‐dienedioate

The title compound, C₁₄H₂₄N₂O₄, consists of two symmetric moieties related through a twofold axis. The whole mol­ecule has a cis conformation. Both the ionic enol form and the non‐ionic keto form make comparable contributions to the structure. In the crystal structure, infinite supramolecular chains are formed through N—H⋯O hydrogen bonds.     

Ammonium di­chloro­bis­(di­methyl­glyoximato‐N,N′)­iridate(III)

In the title compound, (NH₄)[IrCl₂(C₄H₇N₂O₂)₂], (I), the Ir atom is octahedrally coordinated by two trans Cl^? and two di­methyl­glyoximate chelate ligands in the equatorial plane. A two‐dimensional hydrogen‐bond network between ammonium cations NH₄⁺ and anionic [IrCl₂(C₄H₇N₂O₂)₂]^? complexes is extended along the bc plane.     

Three methoxy‐substituted diethyl 4‐­phenyl‐2,6‐di­methyl‐1,4‐di­hydro­pyridine‐3,5‐di­carboxyl­ate compounds

Diethyl 4‐(2,5‐di­methoxy­phenyl)‐2,6‐di­methyl‐1,4‐di­hydro­pyridine‐3,5‐di­carboxyl­ate, C₂₁H₂₇NO₆, (I), diethyl 4‐(3,4‐di­methoxy­phenyl)‐2,6‐di­methyl‐1,4‐di­hydro­pyridine‐3,5‐di­carboxyl­ate, C₂₁H₂₇NO₆, (II), and diethyl 2,6‐di­methyl‐4‐(3,4,5‐tri­methoxy­phenyl)‐1,4‐di­hydro­pyridine‐3,5‐di­carboxyl­ate, C₂₂H₂₉NO₇, (III), crystallize with hydrogen‐bonding networks involving the H atom bonded to the N atom of the 1,4‐di­hydro­pyridine ring and carbonyl O atoms in (I) and (II). Unusually, (III) shows O atoms of methoxy groups serving as hydrogen‐bond acceptors.